Inspection of three-dimensional structures of proteins with dynamical information from the normal mode analysis.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

In this paper it is demonstrated that, to analyze structural data of proteins obtained from X-ray crystallography, the normal mode analysis in dihedral angle space can serve to supplement X-ray data as a useful system for gaining information on their dynamical as well as static structures. Especially, the following two subjects are discussed; first, the breakdown of the motions of a limited region in a polypeptide chain (e.g., an alpha-helix, a beta-strand or a loop) into internal and external motions reveals whether the region is flexible, or it is rigid but mobile when it has large fluctuations. Second, the correlation map between atomic motions serves to provide information for dividing the chain into segments, such as domains or modules, from a dynamical rather than from a geometrical point of view. It is shown that the modules proposed by M. Go appear distinctly in the correlation map as the regions in which clusters of atoms with positive correlation coefficients of their movements to each other exist. Furthermore, the modules are characterized by the negative correlation coefficients of the movements of the atoms in the clusters in a particular module to such movements in a different module.

Original languageEnglish
Pages (from-to)175-180
Number of pages6
JournalProtein sequences & data analysis
Volume2
Issue number3
Publication statusPublished - 1989 Apr

Fingerprint

Proteins
X Ray Crystallography
Information Systems
X-Rays
Peptides
beta-Strand Protein Conformation
alpha-Helical Protein Conformation

ASJC Scopus subject areas

  • Medicine(all)

Cite this

@article{c50e08659b2849aab3de7d15ffac1402,
title = "Inspection of three-dimensional structures of proteins with dynamical information from the normal mode analysis.",
abstract = "In this paper it is demonstrated that, to analyze structural data of proteins obtained from X-ray crystallography, the normal mode analysis in dihedral angle space can serve to supplement X-ray data as a useful system for gaining information on their dynamical as well as static structures. Especially, the following two subjects are discussed; first, the breakdown of the motions of a limited region in a polypeptide chain (e.g., an alpha-helix, a beta-strand or a loop) into internal and external motions reveals whether the region is flexible, or it is rigid but mobile when it has large fluctuations. Second, the correlation map between atomic motions serves to provide information for dividing the chain into segments, such as domains or modules, from a dynamical rather than from a geometrical point of view. It is shown that the modules proposed by M. Go appear distinctly in the correlation map as the regions in which clusters of atoms with positive correlation coefficients of their movements to each other exist. Furthermore, the modules are characterized by the negative correlation coefficients of the movements of the atoms in the clusters in a particular module to such movements in a different module.",
author = "Hiroshi Wako",
year = "1989",
month = "4",
language = "English",
volume = "2",
pages = "175--180",
journal = "Protein sequences & data analysis",
issn = "0931-9506",
number = "3",

}

TY - JOUR

T1 - Inspection of three-dimensional structures of proteins with dynamical information from the normal mode analysis.

AU - Wako, Hiroshi

PY - 1989/4

Y1 - 1989/4

N2 - In this paper it is demonstrated that, to analyze structural data of proteins obtained from X-ray crystallography, the normal mode analysis in dihedral angle space can serve to supplement X-ray data as a useful system for gaining information on their dynamical as well as static structures. Especially, the following two subjects are discussed; first, the breakdown of the motions of a limited region in a polypeptide chain (e.g., an alpha-helix, a beta-strand or a loop) into internal and external motions reveals whether the region is flexible, or it is rigid but mobile when it has large fluctuations. Second, the correlation map between atomic motions serves to provide information for dividing the chain into segments, such as domains or modules, from a dynamical rather than from a geometrical point of view. It is shown that the modules proposed by M. Go appear distinctly in the correlation map as the regions in which clusters of atoms with positive correlation coefficients of their movements to each other exist. Furthermore, the modules are characterized by the negative correlation coefficients of the movements of the atoms in the clusters in a particular module to such movements in a different module.

AB - In this paper it is demonstrated that, to analyze structural data of proteins obtained from X-ray crystallography, the normal mode analysis in dihedral angle space can serve to supplement X-ray data as a useful system for gaining information on their dynamical as well as static structures. Especially, the following two subjects are discussed; first, the breakdown of the motions of a limited region in a polypeptide chain (e.g., an alpha-helix, a beta-strand or a loop) into internal and external motions reveals whether the region is flexible, or it is rigid but mobile when it has large fluctuations. Second, the correlation map between atomic motions serves to provide information for dividing the chain into segments, such as domains or modules, from a dynamical rather than from a geometrical point of view. It is shown that the modules proposed by M. Go appear distinctly in the correlation map as the regions in which clusters of atoms with positive correlation coefficients of their movements to each other exist. Furthermore, the modules are characterized by the negative correlation coefficients of the movements of the atoms in the clusters in a particular module to such movements in a different module.

UR - http://www.scopus.com/inward/record.url?scp=0024644039&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0024644039&partnerID=8YFLogxK

M3 - Article

VL - 2

SP - 175

EP - 180

JO - Protein sequences & data analysis

JF - Protein sequences & data analysis

SN - 0931-9506

IS - 3

ER -